Applied a subdivision modifier and imported in Substance Painter 2, the result is horrible
You should get all the faces that are meant to be flat together as one face. The bottom face on the cylinder in your case should look like a flat face, but because it's made out of a lot of faces, it doesn't. 
Select one of the bottom faces:
 

press Ctrl+Shift+Alt+F to select all the faces that are on a 0 degree angle of it:
 
Now hit X and choose 'Dissolve faces'. Now you have erased the unnecessary vertices: